The Hydrogen Bond by L8Z7qOF

VIEWS: 17 PAGES: 54

									                                                   The Hydrogen Bond
Department of Chemistry, University of Jyväskylä




                                                                     Jan Lundell
                                                    Department of Chemistry, University of Jyväskylä
Department of Chemistry, University of Jyväskylä




                                                   The Hydrogen Bond
                                                                 The Hydrogen Bond
Department of Chemistry, University of Jyväskylä




                                                   Adenine           Thymine




                                                       Guanine       Cytosine


                                                                                Peter Agre (Nobel Prize, 2003):
                                                                                The purest form of hydrogen bond there is…
                                                          The Hydrogen Bond

                                                   ”The hydrogen nucleus held by two octets constitutes a weak
                                                   bond”

                                                        W.M.Latimer and W.H.Rodebush, JACS 42, 1920, 1419
Department of Chemistry, University of Jyväskylä




                                                   ”Under certain conditions an atom of hydrogen is attracted by
                                                   rather strong forces to two atoms instead of only one, so that
                                                   it may be considered to be acting as a bond between them.
                                                   This is called a hydrogen bond.”

                                                        L. Pauling, Nature of Chemical Bond, 1939
                                                                The Hydrogen Bond
                                                                HCOOH in the gas phase – IR ( from webbook.nist.gov )
                                                   Absorbance
Department of Chemistry, University of Jyväskylä




                                                                           Wavenumber
                                                          The Hydrogen Bond

                                                   ”A hydrogen bond exists between the functional group, A-H,
                                                   and an atom or a group of atoms, B,
                                                   in the same or different molecules when

                                                   (a) there is evidence of bond formation (association or
                                                   chelation)
Department of Chemistry, University of Jyväskylä




                                                   (b) there is evidence that this new bond linking A-H and B
                                                   specifically involves a hydrogen atom already bonded to A”

                                                        G.C.Pimentel, A.L.McClellan, The Hydrogen Bond, 1960
                                                               The Hydrogen Bond

                                                                     Strong         Medium        Weak

                                                   bond distance    A-H  H...B   A-H < H...B   A-H << H...B


                                                   H...B (Å)        1.2 - 1.5    1.5 - 2.2    2.2 - 3.2
Department of Chemistry, University of Jyväskylä




                                                   A...B (Å)        2.2 - 2.5     2.5 - 3.2     3.2 - 4.0


                                                   bond angle (º)   175 - 180     130 - 180     90 - 150


                                                   binding energy   60 - 170      15 - 60       < 15
                                                   (kJ/mol)
                                                         The Hydrogen Bond

                                                        Strong              Medium            Weak

                                                   dimers of strong     acids            dimers of weak
                                                   acids and bases in                    acids and bases in
                                                   the gas phase                         the gas phase
Department of Chemistry, University of Jyväskylä




                                                   Acid salts           alcohols,        C-H...O/N
                                                                        phenols

                                                   Proton sponges       hydrates         O/N-H...


                                                   HF complexes         all biological   dihydrogen bonds
                                                                        molecules
                                                                The Hydrogen Bond

                                                        ”A hydrogen atom with only one stable orbital cannot form
                                                        more than one pure covalent bond and
                                                        the attraction of the two atoms observed in hydrogen bond
                                                        formation must be due largely to ionic forces””
Department of Chemistry, University of Jyväskylä




                                                           L.Pauling, The Nature of Chemical Bond, 1939




                                                                        d+
                                                                             d+
                                                   d-      d+

                                                                   d-

                                                   d+
                                                              The Hydrogen Bond
                                                        YHB = aYa + bYb + cYc + dYd + eYe

                                                   Ya       A-H…B              covalent A-H bond
                                                   Yb       A- -H+ …B          ionic A-H bond
                                                   Yc       A- -H…B+           charge transfer , A…B bond
                                                   Yd       A+ -H- …B          ionic A-H bond
                                                   Ya       A-H- …B+           charge transfer, H…B bond
Department of Chemistry, University of Jyväskylä




                                                            C.A.Coulson, In Hydrogen Bonding, D.Hadzi (Ed.) 1959, pp. 339-360.




                                                                                     O-H … O with O … O = 2.8 Å

                                                                                     Yb + Yd contribute 65 % of the hydrogen bond energy
                                                   Interaction energy of a H-bond
                                                   Supermolecular approach
                                                   Eint = EAB – (EA + EB)
Department of Chemistry, University of Jyväskylä
Department of Chemistry, University of Jyväskylä


                                                     Interaction energy
                                                   decomposition scheme
                                                       HCN…HCN ( MP2 )
Department of Chemistry, University of Jyväskylä




                                                   A.Heikkilä, J.Lundell, J.Phys.Chem. A 104, 2000, 6637-6643
                                                           Symmetry-Adapted
                                                       Perturbation Theory (SAPT)
Department of Chemistry, University of Jyväskylä




                                                   K.Szalewicz, K.Patkowski, B.Jeziorski ,Struct.Chem. 116, 2005, 43-117
Department of Chemistry, University of Jyväskylä




                                                   R.A.Christie, K.D.Jordan, Struct.Chem. 116, 2005, 27-41
                                                   Having more than two molecules?
Department of Chemistry, University of Jyväskylä




                                                        S.S.Xantheas Struct.Chem. 116, 2005, 119-148
Department of Chemistry, University of Jyväskylä
Department of Chemistry, University of Jyväskylä
Department of Chemistry, University of Jyväskylä




   S.S.Xantheas Struct.Chem. 116, 2005, 119-148
Department of Chemistry, University of Jyväskylä

                                                   Non-additive (cooperative) effects
Department of Chemistry, University of Jyväskylä




   S.S.Xantheas Struct.Chem. 116, 2005, 119-148
                                                            Basis set superposition error
                                                                       (BSSE)
                                                         Not perfect basis sets, so needs to borrow
                                                         from the neighbour…

                                                                                              HNC…HCN
Department of Chemistry, University of Jyväskylä




                                                   The ”cure”:
                                                   Counterpoise correction (Boys-Bernardi )
Department of Chemistry, University of Jyväskylä
Department of Chemistry, University of Jyväskylä
Department of Chemistry, University of Jyväskylä




S.S.Xantheas Struct.Chem. 116, 2005, 119-148
Department of Chemistry, University of Jyväskylä




                                                   J.R.Lane, H.G.Kjaergaard, J.Phys.Chem. 131, 2009, 034307
                                                   Changes upon hydrogen bonding…
Department of Chemistry, University of Jyväskylä




                                                       G.A.Jeffrey, An Introduction to Hydrogen Bonding, 1997
                                                   HCOOH photochemistry in matrices



                                                                                                                        H2O + CO
                                                             hn
Department of Chemistry, University of Jyväskylä




                                                   t-HCOOH                                                                 vs
                                                                                                                        CO2 + H2




                                                                  J.Lundell, M.Räsänen, J.Phys.Chem. 99, 1995, 14301.
                                                   H2O...CO : Two stable complex
                                                             structures
                                                                              CCSD(T)/6-311++G(2d,2p)
Department of Chemistry, University of Jyväskylä




                                                                        2.365                                                    2.323




                                                   Eint,cp = -5.29 kJ mol-1                                  Eint,cp = -3.17 kJ mol-1




                                                                          J.Lundell, J.Phys.Chem. 99, 1995,14290
                                                                          J.Lundell, Z.Latajka, J.Phys.Chem. A 101, 1997, 5004
                                                        H2O...CO : Experiments
                                                   In situ photolysis of formic acid in a solid
                                                   argon matrix
                                                                                          HOH...CO
                                                                              exp.       Dn         calc.      Dw

                                                                              3724       -9         3864       -17
Department of Chemistry, University of Jyväskylä




                                                                              3628       -9         3826       -22

                                                                              1596       +2         1656       +10



                                                                              2148       +10        2130       +13

                                                                               JPC 99, 1995, 14290: MP2/6-311++G(2d,2p)
                                                                               JPC 99, 1995, 14301: Ng-matrices
                                                       H2O...CO : Experiments
                                                   Annealing the matrix after photolysis

                                                   argon             krypton               xenon
Department of Chemistry, University of Jyväskylä
                                                      H2O...CO : Experiments

                                                   Both HOH...CO and HOH...OC can be made

                                                      CO stretch            HOH...CO    HOH...OC

                                                      Gas phase             2154   +11
Department of Chemistry, University of Jyväskylä




                                                      Ar                    2149   +11

                                                      Kr                    2145   +9    2130   -6

                                                      Xe                    2142   +8    2128   -5

                                                      calc.                 2130   +10   2118   -2
                                                      MP2/6-311++G(2d,2p)
                                                                                   Can we do more?
                                                            HOD ... CO

                                                     0. 3
                                                                                                                                         1.0

                                                                        nOH free                                                                                       nOD bond
                                                     0. 2

                                                   E                                                                                     0.5
                                                   m
                                                   i
                                                                                   ?                                                   E
                                                                                                                                       m
                                                                                                                                                         ?
                                                   s 0. 1                                                                              i
                                                   s                                                                                   s
                                                   i                                                                                   s 0.0
                                                   v                                                                                   i
                                                   i 0. 0                                                                              v
                                                   t                                                                                   i
                                                   y                                                                                   t
                                                                                                                                       y-0.5
Department of Chemistry, University of Jyväskylä




                                                    -0.1



                                                                                                                                        -1.0
                                                    -0.2


                                                                         3720               3700               3680             3660
                                                                                                                                                  2780   2760   2740          2720          2700    2680
                                                                                           Wavenumbers
                                                                                                                                                                Wavenumbers




                                                                           nOH free                                                    0.7
                                                                                                                                                                           nOD bond
                                                   E 32
                                                   -0.                                                                                 E
                                                   m                                                                                   m
                                                   i                                                                                   i 0.6
                                                   s                                                                                   s
                                                   s                                                                                   s
                                                   i                                                                                   i
                                                   -0.
                                                   v 34                                                                                v
                                                   i                                                                                   i 0.5
                                                   t                                                                                   t
                                                   y                                                                                   y


                                                   -0. 36
                                                                                                                                        0.4                                                   ?

                                                   -0. 38                                                                               0.3
                                                        73 20   73 00      72 80   72 60           72 40   72 20      72 00   71 80            5700      5600      5500              5400          5300
                                                                                           Wa venumbers                                                         Wavenumbers
                                                   Anharmonic calculations: cc-VSCF

                                                    Vibrational Schrödinger equation in mass-
                                                    weighted normal mode coordinates

                                                              1 N 2                   
                                                                2  V (Q1 ,..., QN )  n (Q1 ,..., QN )  En n (Q1 ,..., QN )
                                                              2 j 1 Q j
                                                                                       
                                                                                        
Department of Chemistry, University of Jyväskylä




                                                      single-mode wavefunctions, energies and
                                                       effective potentials
                                                       2nd order perturbation theory for correlation effects
                                                        between different vibrational modes
                                                       pairwise interactions between normal modes
                                                   Anharmonic calculations: cc-VSCF

                                                    Grid-approach of PES:
                                                    - 8  8 or 16  16 grids
                                                    - points chosen equidistantly over an interval defined by the
                                                    harmonic frequency of a vibrational mode:
                                                    Qmax ~ inverse square root of the frequency
Department of Chemistry, University of Jyväskylä




                                                    G.M.Chaban, J.O.Jung, R.B.Gerber, J.Phys.Chem. A 104, 2000, 2772




                                                    Implemented in GAMESS-US
Department of Chemistry, University of Jyväskylä


                                                   MP2/aug-cc-pVTZ + cc-VSCF




  * CO2...H2
Department of Chemistry, University of Jyväskylä


                                                   MP2/aug-cc-pVTZ + cc-VSCF
Department of Chemistry, University of Jyväskylä
                                                                                  The formic acid monomer:
                                                                                       Two conformers


                                                                                                      MP2/6-311++G(2d,2p)
                                                                           5000


                                                                           4000
                                                   Relative energy [cm ]
                                                   -1
Department of Chemistry, University of Jyväskylä




                                                                                                                                              cis
                                                                           3000

                                                                                      trans
                                                                           2000
                                                                                                         4544 cm-1
                                                                                                    Exp: 4842 cm-1
                                                                           1000
                                                                                                                                 1488 cm-1
                                                                                                                             Exp: 1362 cm-1
                                                                             0

                                                                                  0      20    40    60    80    100   120   140   160   180
                                                                                              O=C-O-H torsional angle [deg]
                                                   IR-pumping at
                                                   6934 cm-1 (2 nOH)




                                                                                                   cis
Department of Chemistry, University of Jyväskylä




                                                           IR




                                                                                                  trans




                                                           M.Pettersson, J.Lundell, L.Khriachtchev, M.Räsänen, JACS 119, 1997, 11715
                                                                                                                           HCOOH
                                                                                                                anharmonic calculations
                                                                                  140
                                                   Computed intensity [km mol ]




                                                                                             trans-HCOOH
                                                                             -1




                                                                                  120

                                                                                  100

                                                                                   80

                                                                                   60      anharmonic
                                                                                   40      harmonic

                                                                                   20

                                                                                    0
Department of Chemistry, University of Jyväskylä




                                                                                    5000      4000       3000    2000    1000


                                                                                  140
                                                                                             cis-HCOOH
                                                   Computed intensity [km mol ]
                                                                             -1




                                                                                  120

                                                                                  100

                                                                                   80

                                                                                   60

                                                                                   40

                                                                                   20

                                                                                    0
                                                                                    5000       4000      3000     2000    1000
                                                                                                                    -1
                                                                                                      Wavenumber [cm ]

                                                    E.M.S.Macoas, J.Lundell, M. Pettersson, L.Khriachtchev, R.Fausto, M.Räsänen,
                                                   J.Mol.Spectrosc. 219, 2003, 70.
                                                          Isomerisation of formic acid:
                                                                 The monomer

                                                                                   vibr exc


                                                                                 tunneling
                                                           trans
                                                                                                            cis
Department of Chemistry, University of Jyväskylä




                                                    Tunneling can be stopped by complexation




                                                                                         X

                                                   K. Marushkevich, L.Khriachtchev, M.Räsänen, J.Phys.Chem. A 111, 2007, 2040
                                                                     The trans-trans formic acid dimers

                                                    FAD-tt1                              FAD-tt3                     FAD-tt5

                                                                1.684                                2.408                    1.896
                                                             1.684                                   2.509
                                                                                                                               2.406


                                                      Ecp,int (MP2)= -66.71 kJ mol-1       Ecp,int (MP2)= -11.81       Ecp,int (MP2)= -23.36
Department of Chemistry, University of Jyväskylä




                                                   FAD-tt2                                FAD-tt4                    FAD-tt6

                                                              1.774                                 1.927                        2.417
                                                                                                     1.968
                                                             2.337                                                              2.417

                                                      Ecp,int (MP2)= -37.21                                             Ecp,int (MP2)= -15.39
                                                                                             Ecp,int (MP2)= -28.68




                                                                                       MP2/6-311++G(2d,2p)
                                                                 The trans-trans –dimer (FAD-tt1)

                                                   FAD-tt1 in solid argon
Department of Chemistry, University of Jyväskylä




                                                   From M.Gantenberg, M.Halupka, W.Sander,
                                                                                             4000   3500    3000     2500     2000     1500     1000    500
                                                   Chem.Eur.J. 6, 2000, 1865
                                                                                                        Computed wavenumber [cm-1]


                                                                                                    MP2/6-311++G(2d,2p) cc-VSCF without mode coupling
                                                   Solid argon

                                                                                         FAD-tt1                 FAD-tt2
Department of Chemistry, University of Jyväskylä




                                                     A.Olbert-Majkut, J.Ahokas, J.Lundell, M.Pettersson, Chem.Phys.Lett. 468, 2009, 176.
                                                                                     The trans-trans formic acid dimers

                                                                                Computed relative energies



                                                                                80                                                   FAD-cc3
                                                                                                                                     FAD-cc4
                                                                                                                 FAD-tc4             FAD-cc2
                                                   Relative energy [kJ mol-1]




                                                                                                                                     FAD-cc1
Department of Chemistry, University of Jyväskylä




                                                                                                                                     FAD-cc5
                                                                                60                               FAD-tc5
                                                                                                     FAD-tt3
                                                                                                     FAD-tt3     FAD-tc3
                                                                                                     FAD-tt6
                                                                                                                 FAD-tc2
                                                                                40                   FAD-tt5     FAD-tc1
                                                                                                     FAD-tt4

                                                                                                     FAD-tt2
                                                                                20        cis-FA



                                                                                                               Experimentally observed
                                                                                 0        trans-FA   FAD-tt1
                                                                                                                                   excitation at
                                                                                                                                   3168 cm-1 (C-H str)
                                                        Pumping O-H str in trans-trans dimer ?

                                                    FAD-tt1 (CD)
                                                                                                                             *




                                                                                                       *
Department of Chemistry, University of Jyväskylä




                                                   Excitation at 3540 cm-1

                                                               *
                                                     FAD-tt2 ( * )



                                                                                                           *                 *




                                                       K.Marushkevich, L.Khriachtchev, J.Lundell, M.Räsänen, JACS 128, 2006, 12060
                                                                         The cis-trans formic acid dimers

                                                    FAD-tc1                               FAD-tc3


                                                                    1.761
                                                                                                     1.814
                                                                 2.287
                                                                                                                        FAD-tc5
                                                        Ecp,int (MP2)= -41.31 kJ mol-1        Ecp,int (MP2)= -29.79
Department of Chemistry, University of Jyväskylä




                                                                                                                                  1.857

                                                                                         FAD-tc4
                                                   FAD-tc2
                                                                                                                              Ecp,int (MP2)= -23.20

                                                                 1.950                                   2.502

                                                                1.852
                                                                                                          2.387


                                                         Ecp,int (MP2)= -38.02
                                                                                                Ecp,int (MP2)= -12.74




                                                                                         MP2/6-311++G(2d,2p)
                                                   The cis-trans formic acid dimers

                                                      1.774
                                                              hn (IR)                           1.761


                                                     2.337                                    2.287



                                                   FAD-tt2                                   FAD-tc1

                                                                  x5                                              x1
Department of Chemistry, University of Jyväskylä




                                                                              FAD-tc1                              FAD-tc1




                                                                        FAD-tt2                                   FAD-tt2




                                                                        trans-FA                                    trans-FA



                                                                3625   3600   3575    3550    3525    3500 1900   1850   1800   1750   1700   1650

                                                                                     cc-VSCF//MP2 computed wavenumbers [cm-1]
                                                                                   The cis-trans formic acid dimers



                                                                                                  4543.7 cm-1           4771.5 cm-1
                                                                                 5000
                                                                                                                                            Mon
                                                                                                                                            Dim
                                                                                 4000
Department of Chemistry, University of Jyväskylä




                                                            Rel. energy [ cm ]
                                                           -1




                                                                                 3000


                                                                                 2000
                                                                                                                                                  1488.0 cm-1

                                                                                 1000


                                                                                    0                                                             1180.3 cm-1

                                                                                        0   20   40   60     80   100    120    140   160   180
                                                                                                      Torsional angle [ deg ]
                                                   MP2/6-311++G(2d,2p)
                                                                                 Photoisomerisation of formic acid dimers:

                                                                                Computed relative energies



                                                                                80
                                                                                                                 FAD-tc4
                                                   Relative energy [kJ mol-1]




                                                                                                                                     FAD-cc1
Department of Chemistry, University of Jyväskylä




                                                                                                                                     FAD-cc5
                                                                                                                                     FAD-cc4
                                                                                60                               FAD-tc5
                                                                                                                                     FAD-cc2
                                                                                                     FAD-tt3     FAD-tc3
                                                                                                     FAD-tt6
                                                                                                                 FAD-tc2
                                                                                40                   FAD-tt5     FAD-tc1
                                                                                                     FAD-tt4

                                                                                                     FAD-tt2
                                                                                20        cis-FA



                                                                                                               Experimentally observed
                                                                                 0        trans-FA   FAD-tt1
                                                                          The cis-cis formic acid dimers


                                                   FAD-cc1                               FAD-cc3

                                                                                                      2.370
                                                                  1.878
                                                                                                      2.370
                                                                  2.765

                                                                                                                     FAD-cc5
                                                                                            Ecp,int (MP2)= -20.95
                                                      Ecp,int (MP2)= -31.82 kJ mol-1
Department of Chemistry, University of Jyväskylä




                                                                                                                                     1.816




                                                   FAD-cc2                                FAD-cc4
                                                                                                                         Ecp,int (MP2)= -31.99

                                                                                                     2.006
                                                                      1.853
                                                                                                        2.684
                                                       Ecp,int (MP2)= -32.10
                                                                                             Ecp,int (MP2)= -24.47




                                                                                       MP2/6-311++G(2d,2p)
                                                                                     The cis-cis formic acid dimers
                                                                                Computed relative energies

                                                                                                                       ?
                                                                                80                                                        FAD-cc3
                                                                                                                                          FAD-cc4
                                                                                                                  FAD-tc4                 FAD-cc2
                                                   Relative energy [kJ mol-1]




                                                                                                                                          FAD-cc1
                                                                                                                                          FAD-cc5
                                                                                60                                FAD-tc5
Department of Chemistry, University of Jyväskylä




                                                                                                      FAD-tt3     FAD-tc3
                                                                                                      FAD-tt6
                                                                                                                  FAD-tc2
                                                                                40                    FAD-tt5
                                                                                                      FAD-tt4
                                                                                                                  FAD-tc1
                                                                                                                                    ?
                                                                                                      FAD-tt2
                                                                                20         cis-FA



                                                                                                                Experimentally observed
                                                                                 0         trans-FA   FAD-tt1
                                                                 Current topics
                                                     (Horizons in Hydrogen Bond Research, Paris, Sept 2009)


                                                   Blue-shifting hydrogen bonds vs
                                                   red-shifting hydrogen bonds

                                                   Dihydrogen bonds              (for example, H-O-H…HXeH )
Department of Chemistry, University of Jyväskylä




                                                   Biomolecular systems
                                                   - Water as biolubricant

                                                   “Fast spectroscopy” (also dynamic simulations )

								
To top